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CHECK report for BiRewire on merida2

This page was generated on 2019-04-09 13:28:38 -0400 (Tue, 09 Apr 2019).

Package 170/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.15.0
Andrea Gobbi
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/BiRewire
Branch: master
Last Commit: 5705c02
Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: BiRewire
Version: 3.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiRewire_3.15.0.tar.gz
StartedAt: 2019-04-08 23:33:52 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:37:42 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 229.5 seconds
RetCode: 0
Status:  OK 
CheckDir: BiRewire.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiRewire_3.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BiRewire.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiRewire/DESCRIPTION’ ... OK
* this is package ‘BiRewire’ version ‘3.15.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiRewire’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
birewire.analysis.bipartite: no visible binding for global variable
  ‘sd’
birewire.analysis.bipartite: no visible global function definition for
  ‘qt’
birewire.analysis.bipartite: no visible global function definition for
  ‘par’
birewire.analysis.bipartite: no visible global function definition for
  ‘plot’
birewire.analysis.bipartite: no visible global function definition for
  ‘polygon’
birewire.analysis.bipartite: no visible global function definition for
  ‘lines’
birewire.analysis.bipartite: no visible global function definition for
  ‘abline’
birewire.analysis.bipartite: no visible global function definition for
  ‘legend’
birewire.analysis.dsg: no visible global function definition for
  ‘dev.off’
birewire.analysis.dsg: no visible binding for global variable ‘sd’
birewire.analysis.dsg: no visible global function definition for ‘qt’
birewire.analysis.dsg: no visible global function definition for ‘plot’
birewire.analysis.dsg: no visible global function definition for
  ‘polygon’
birewire.analysis.dsg: no visible global function definition for
  ‘lines’
birewire.analysis.dsg: no visible global function definition for
  ‘abline’
birewire.analysis.dsg: no visible global function definition for
  ‘legend’
birewire.analysis.undirected: no visible binding for global variable
  ‘sd’
birewire.analysis.undirected: no visible global function definition for
  ‘qt’
birewire.analysis.undirected: no visible global function definition for
  ‘par’
birewire.analysis.undirected: no visible global function definition for
  ‘plot’
birewire.analysis.undirected: no visible global function definition for
  ‘polygon’
birewire.analysis.undirected: no visible global function definition for
  ‘lines’
birewire.analysis.undirected: no visible global function definition for
  ‘abline’
birewire.analysis.undirected: no visible global function definition for
  ‘legend’
birewire.load.dsg: no visible global function definition for
  ‘read.table’
birewire.sampler.bipartite: no visible global function definition for
  ‘write.table’
birewire.sampler.undirected: no visible global function definition for
  ‘write.table’
birewire.save.dsg: no visible global function definition for
  ‘write.table’
birewire.visual.monitoring.bipartite: no visible global function
  definition for ‘par’
birewire.visual.monitoring.bipartite: no visible global function
  definition for ‘plot’
birewire.visual.monitoring.bipartite: no visible global function
  definition for ‘colorRampPalette’
birewire.visual.monitoring.bipartite: no visible global function
  definition for ‘text’
birewire.visual.monitoring.dsg: no visible global function definition
  for ‘par’
birewire.visual.monitoring.dsg: no visible global function definition
  for ‘plot’
birewire.visual.monitoring.dsg: no visible global function definition
  for ‘colorRampPalette’
birewire.visual.monitoring.dsg: no visible global function definition
  for ‘text’
birewire.visual.monitoring.undirected: no visible global function
  definition for ‘par’
birewire.visual.monitoring.undirected: no visible global function
  definition for ‘plot’
birewire.visual.monitoring.undirected: no visible global function
  definition for ‘colorRampPalette’
birewire.visual.monitoring.undirected: no visible global function
  definition for ‘text’
Undefined global functions or variables:
  abline colorRampPalette dev.off legend lines par plot polygon qt
  read.table sd text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "polygon", "text")
  importFrom("stats", "qt", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                        user system elapsed
birewire.analysis.undirected          70.436  0.180  71.118
birewire.visual.monitoring.dsg        49.619  0.443  50.438
birewire.visual.monitoring.undirected 16.486  1.241  17.907
birewire.visual.monitoring.bipartite   7.944  0.063   8.069
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/BiRewire.Rcheck/00check.log’
for details.



Installation output

BiRewire.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiRewire
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘BiRewire’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BiRewire.c -o BiRewire.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c interface.c -o interface.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BiRewire/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiRewire)

Tests output

BiRewire.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require(BiRewire) || stop("unable to load MyPackage")
Loading required package: BiRewire
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: slam
Loading required package: tsne
Loading required package: Matrix
[1] TRUE
> BiocGenerics:::testPackage('BiRewire')
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[1] "You are using a matrix with NA. It is strongly suggested to use MAXITER_MUL=100 and exact=TRUE because the number of configuration with the NA constrain can terribly decrease, the routine will use  these."
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[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.5939273220175
Epoch: Iteration #200 error is: 0.334066189787335
Epoch: Iteration #300 error is: 0.258602082426953
Epoch: Iteration #400 error is: 0.253780466191295
Epoch: Iteration #500 error is: 0.253249107834644
Epoch: Iteration #600 error is: 0.251950405011713
Epoch: Iteration #700 error is: 0.251938603496339
Epoch: Iteration #800 error is: 0.251937446581898
Epoch: Iteration #900 error is: 0.25193725835856
Epoch: Iteration #1000 error is: 0.25193724650157
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 12.7148949956528
Epoch: Iteration #200 error is: 0.345073983409189
Epoch: Iteration #300 error is: 0.261188771672243
Epoch: Iteration #400 error is: 0.253320551446277
Epoch: Iteration #500 error is: 0.25208103444718
Epoch: Iteration #600 error is: 0.251937784348884
Epoch: Iteration #700 error is: 0.251937340091635
Epoch: Iteration #800 error is: 0.251937243523398
Epoch: Iteration #900 error is: 0.25193722823234
Epoch: Iteration #1000 error is: 0.251937227284472
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.2208759906646
Epoch: Iteration #200 error is: 0.284781527885421
Epoch: Iteration #300 error is: 0.258355047955345
Epoch: Iteration #400 error is: 0.251961365419537
Epoch: Iteration #500 error is: 0.25193645888893
Epoch: Iteration #600 error is: 0.251935797407255
Epoch: Iteration #700 error is: 0.251935796458354
Epoch: Iteration #800 error is: 0.251935796264655
Epoch: Iteration #900 error is: 0.251935795982952
Epoch: Iteration #1000 error is: 0.251935795617262
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 10.436271512001
Epoch: Iteration #200 error is: 0.301938014977008
Epoch: Iteration #300 error is: 0.257107314382038
Epoch: Iteration #400 error is: 0.254199409429257
Epoch: Iteration #500 error is: 0.251971420232972
Epoch: Iteration #600 error is: 0.251939341995345
Epoch: Iteration #700 error is: 0.251936702354229
Epoch: Iteration #800 error is: 0.251936559447012
Epoch: Iteration #900 error is: 0.251936558146158
Epoch: Iteration #1000 error is: 0.251936558081574
[1] "K= 1"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.4301067396012
Epoch: Iteration #200 error is: 0.33273279045277
Epoch: Iteration #300 error is: 0.255552442080192
Epoch: Iteration #400 error is: 0.252037029174256
Epoch: Iteration #500 error is: 0.251939722898334
Epoch: Iteration #600 error is: 0.251936718599624
Epoch: Iteration #700 error is: 0.251936507296488
Epoch: Iteration #800 error is: 0.251936504774937
Epoch: Iteration #900 error is: 0.251936504695838
Epoch: Iteration #1000 error is: 0.251936504598589
[1] "K= 5"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 11.1213878512746
Epoch: Iteration #200 error is: 0.299211598650134
Epoch: Iteration #300 error is: 0.252108767597199
Epoch: Iteration #400 error is: 0.250843307461883
Epoch: Iteration #500 error is: 0.250829800266134
Epoch: Iteration #600 error is: 0.25082961120559
Epoch: Iteration #700 error is: 0.250829309813843
Epoch: Iteration #800 error is: 0.250828899908928
Epoch: Iteration #900 error is: 0.250828412379691
Epoch: Iteration #1000 error is: 0.250827908667504
[1] "K= 100"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 13.6743494911673
Epoch: Iteration #200 error is: 0.432223408243428
Epoch: Iteration #300 error is: 0.263302976271566
Epoch: Iteration #400 error is: 0.252451299271298
Epoch: Iteration #500 error is: 0.251956744498196
Epoch: Iteration #600 error is: 0.25193822074166
Epoch: Iteration #700 error is: 0.251937841898127
Epoch: Iteration #800 error is: 0.251937703438561
Epoch: Iteration #900 error is: 0.251937654774993
Epoch: Iteration #1000 error is: 0.251937644938676
[1] "K= n"
sigma summary: Min. : 33554432 |1st Qu. : 33554432 |Median : 33554432 |Mean : 33554432 |3rd Qu. : 33554432 |Max. : 33554432 |
Epoch: Iteration #100 error is: 16.9425601744292
Epoch: Iteration #200 error is: 0.489737608979669
Epoch: Iteration #300 error is: 0.289898224468982
Epoch: Iteration #400 error is: 0.271265040042594
Epoch: Iteration #500 error is: 0.259540152774736
Epoch: Iteration #600 error is: 0.25357585047638
Epoch: Iteration #700 error is: 0.25268133259834
Epoch: Iteration #800 error is: 0.252317356064175
Epoch: Iteration #900 error is: 0.252151860452185
Epoch: Iteration #1000 error is: 0.252043868292934


RUNIT TEST PROTOCOL -- Mon Apr  8 23:37:36 2019 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiRewire RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 23.551   1.223  24.903 

Example timings

BiRewire.Rcheck/BiRewire-Ex.timings

nameusersystemelapsed
birewire.analysis.bipartite0.1740.1550.332
birewire.analysis.dsg0.0860.0160.102
birewire.analysis.undirected70.436 0.18071.118
birewire.bipartite.from.incidence0.0120.0160.028
birewire.build.dsg0.0120.0010.014
birewire.induced.bipartite0.0030.0010.004
birewire.rewire.bipartite0.0110.0130.024
birewire.rewire.bipartite.and.projections0.1270.0070.135
birewire.rewire.dsg0.0040.0010.005
birewire.rewire.undirected0.7990.0570.859
birewire.similarity0.0110.0010.011
birewire.similarity.dsg0.0280.0020.030
birewire.visual.monitoring.bipartite7.9440.0638.069
birewire.visual.monitoring.dsg49.619 0.44350.438
birewire.visual.monitoring.undirected16.486 1.24117.907